Environment-like API for Bimap objects

Description

These methods allow the user to manipulate any Bimap object as if it was an environment. This environment-like API is provided for backward compatibility with the traditional environment-based maps.

Usage

  ls(name, pos = -1L, envir = as.environment(pos), all.names = FALSE,
     pattern, sorted = TRUE)
  exists(x, where, envir, frame, mode, inherits)
  get(x, pos, envir, mode, inherits)
  #x[[i]]
  #x$name

  ## Converting to a list
  mget(x, envir, mode, ifnotfound, inherits)
  eapply(env, FUN, ..., all.names, USE.NAMES)
  #contents(object, all.names)

  ## Additional convenience method
  sample(x, size, replace=FALSE, prob=NULL, ...)

Arguments

See Also

ls, exists, get, mget, eapply, contents, sample, BimapFormatting, Bimap

Examples

  library(hgu95av2.db)
  x <- hgu95av2CHRLOC

  ls(x)[1:3]
  exists(ls(x)[1], x)
  exists("titi", x)
  get(ls(x)[1], x)
  x[[ls(x)[1]]]
  x$titi # NULL

  mget(ls(x)[1:3], x)
  eapply(x, length)
  contents(x)

  sample(x, 3)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(AnnotationDbi)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AnnotationDbi/Bimap-envirAPI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bimap-envirAPI
> ### Title: Environment-like API for Bimap objects
> ### Aliases: Bimap-envirAPI ls ls,Bimap-method exists
> ###   exists,ANY,ANY,Bimap-method exists,ANY,Bimap,missing-method get
> ###   get,ANY,ANY,Bimap-method get,ANY,Bimap,missing-method [[,Bimap-method
> ###   $,Bimap-method mget mget,Bimap-method mget,ANY,Bimap-method eapply
> ###   eapply,Bimap-method contents,Bimap-method sample sample,Bimap-method
> ###   sample,environment-method
> ### Keywords: methods interface
> 
> ### ** Examples
> 
>   library(hgu95av2.db)
Loading required package: org.Hs.eg.db


>   x <- hgu95av2CHRLOC
> 
>   ls(x)[1:3]
[1] "1000_at"   "1001_at"   "1002_f_at"
>   exists(ls(x)[1], x)
[1] TRUE
>   exists("titi", x)
[1] FALSE
>   get(ls(x)[1], x)
       16        16 
-30125425 -30128157 
>   x[[ls(x)[1]]]
       16        16 
-30125425 -30128157 
>   x$titi # NULL
NULL
> 
>   mget(ls(x)[1:3], x)
$`1000_at`
       16        16 
-30125425 -30128157 

$`1001_at`
       1 
43766565 

$`1002_f_at`
      10 
96522437 

>   eapply(x, length)
$`1000_at`
[1] 2

$`1001_at`
[1] 1

$`1002_f_at`
[1] 1

$`1003_s_at`
[1] 2

$`1004_at`
[1] 2

$`1005_at`
[1] 1

$`1006_at`
[1] 1

$`1007_s_at`
[1] 1

$`1008_f_at`
[1] 2

$`1009_at`
[1] 1

$`100_g_at`
[1] 1

$`1010_at`
[1] 1

$`1011_s_at`
[1] 1

$`1012_at`
[1] 1

$`1013_at`
[1] 1

$`1014_at`
[1] 1

$`1015_s_at`
[1] 2

$`1016_s_at`
[1] 1

$`1017_at`
[1] 2

$`1018_at`
[1] 1

$`1019_g_at`
[1] 1

$`101_at`
[1] 3

$`1020_s_at`
[1] 3

$`1021_at`
[1] 1

$`1022_f_at`
[1] 1

$`1023_at`
[1] 1

$`1024_at`
[1] 1

$`1025_g_at`
[1] 1

$`1026_s_at`
[1] 14

$`1027_at`
[1] 14

$`1028_at`
[1] 1

$`1029_s_at`
[1] 1

$`102_at`
[1] 3

$`1030_s_at`
[1] 1

$`1031_at`
[1] 1

$`1032_at`
[1] 2

$`1033_g_at`
[1] 2

$`1034_at`
[1] 1

$`1035_g_at`
[1] 1

$`1036_at`
[1] 1

$`1037_at`
[1] 1

$`1038_s_at`
[1] 1

$`1039_s_at`
[1] 2

$`103_at`
[1] 3

$`1040_s_at`
[1] 2

$`1041_at`
[1] 1

$`1042_at`
[1] 2

$`1043_s_at`
[1] 4

$`1044_s_at`
[1] 2

$`1045_s_at`
[1] 1

$`1046_at`
[1] 1

$`1047_s_at`
[1] 1

$`1048_at`
[1] 3

$`1049_g_at`
[1] 3

$`104_at`
[1] 2

$`1050_at`
[1] 1

$`1051_g_at`
[1] 1

$`1052_s_at`
[1] 1

$`1053_at`
[1] 1

$`1054_at`
[1] 2

$`1055_g_at`
[1] 2

$`1056_s_at`
[1] 3

$`1057_at`
[1] 2

$`1058_at`
[1] 1

$`1059_at`
[1] 2

$`105_at`
[1] 1

$`1060_g_at`
[1] 2

$`1061_at`
[1] 1

$`1062_g_at`
[1] 1

$`1063_s_at`
[1] 1

$`1064_at`
[1] 1

$`1065_at`
[1] 1

$`1066_at`
[1] 3

$`1067_at`
[1] 2

$`1068_g_at`
[1] 2

$`1069_at`
[1] 1

$`106_at`
[1] 2

$`1070_at`
[1] 1

$`1071_at`
[1] 3

$`1072_g_at`
[1] 3

$`1073_at`
[1] 1

$`1074_at`
[1] 1

$`1075_f_at`
[1] 1

$`1076_at`
[1] 1

$`1077_at`
[1] 1

$`1078_at`
[1] 4

$`1079_g_at`
[1] 4

$`107_at`
[1] 1

$`1080_s_at`
[1] 1

$`1081_at`
[1] 2

$`1082_at`
[1] 1

$`1083_s_at`
[1] 1

$`1084_at`
[1] 3

$`1085_s_at`
[1] 1

$`1086_at`
[1] 1

$`1087_at`
[1] 1

$`1088_at`
[1] 9

$`1089_i_at`
[1] 1

$`108_g_at`
[1] 1

$`1090_f_at`
[1] 1

$`1091_at`
[1] 5

$`1092_at`
[1] 1

$`1093_at`
[1] 2

$`1094_g_at`
[1] 2

$`1095_s_at`
[1] 3

$`1096_g_at`
[1] 1

$`1097_s_at`
[1] 3

$`1098_at`
[1] 2

$`1099_s_at`
[1] 1

$`109_at`
[1] 2

$`1100_at`
[1] 1

$`1101_at`
[1] 6

$`1102_s_at`
[1] 4

$`1103_at`
[1] 2

$`1104_s_at`
[1] 1

$`1105_s_at`
[1] 1

$`1106_s_at`
[1] 1

$`1107_s_at`
[1] 1

$`1108_s_at`
[1] 1

$`1109_s_at`
[1] 1

$`110_at`
[1] 1

$`1110_at`
[1] 1

$`1111_at`
[1] 2

$`1112_g_at`
[1] 2

$`1113_at`
[1] 1

$`1114_at`
[1] 2

$`1115_at`
[1] 1

$`1116_at`
[1] 1

$`1117_at`
[1] 1

$`1118_at`
[1] 1

$`1119_at`
[1] 1

$`111_at`
[1] 1

$`1120_at`
[1] 1

$`1121_g_at`
[1] 1

$`1122_f_at`
[1] 1

$`1123_at`
[1] 1

$`1124_at`
[1] 1

$`1125_s_at`
[1] 2

$`1126_s_at`
[1] 2

$`1127_at`
[1] 2

$`1128_s_at`
[1] 1

$`1129_at`
[1] 1

$`112_g_at`
[1] 3

$`1130_at`
[1] 1

$`1131_at`
[1] 1

$`1132_s_at`
[1] 2

$`1133_at`
[1] 1

$`1134_at`
[1] 3

$`1135_at`
[1] 1

$`1136_at`
[1] 1

$`1137_at`
[1] 3

$`1138_at`
[1] 1

$`1139_at`
[1] 2

$`113_i_at`
[1] 2

$`1140_at`
[1] 1

$`1141_at`
[1] 1

$`1142_at`
[1] 1

$`1143_s_at`
[1] 6

$`1144_at`
[1] 6

$`1145_g_at`
[1] 6

$`1146_at`
[1] 1

$`1147_at`
[1] 1

$`1148_s_at`
[1] 8

$`1149_at`
[1] 4

$`114_r_at`
[1] 2

$`1150_at`
[1] 2

$`1151_at`
[1] 1

$`1152_i_at`
[1] 1

$`1153_f_at`
[1] 1

$`1154_at`
[1] 1

$`1155_at`
[1] 1

$`1156_at`
[1] 2

$`1157_s_at`
[1] 1

$`1158_s_at`
[1] 1

$`1159_at`
[1] 1

$`115_at`
[1] 1

$`1160_at`
[1] 1

$`1161_at`
[1] 2

$`1162_g_at`
[1] 8

$`1163_at`
[1] 2

$`1164_at`
[1] 1

$`1165_at`
[1] 1

$`1166_at`
[1] 2

$`1167_s_at`
[1] 1

$`1168_at`
[1] 1

$`1169_at`
[1] 2

$`116_at`
[1] 1

$`1170_at`
[1] 3

$`1171_s_at`
[1] 3

$`1172_at`
[1] 1

$`1173_g_at`
[1] 1

$`1174_at`
[1] 1

$`1175_s_at`
[1] 1

$`1176_at`
[1] 1

$`1177_at`
[1] 1

$`1178_at`
[1] 1

$`1179_at`
[1] 1

$`117_at`
[1] 1

$`1180_g_at`
[1] 1

$`1181_at`
[1] 8

$`1182_at`
[1] 1

$`1183_at`
[1] 1

$`1184_at`
[1] 1

$`1185_at`
[1] 2

$`1186_at`
[1] 1

$`1187_at`
[1] 2

$`1188_g_at`
[1] 2

$`1189_at`
[1] 1

$`118_at`
[1] 1

$`1190_at`
[1] 2

$`1191_s_at`
[1] 1

$`1192_at`
[1] 1

$`1193_at`
[1] 2

$`1194_g_at`
[1] 2

$`1195_s_at`
[1] 1

$`1196_at`
[1] 2

$`1197_at`
[1] 1

$`1198_at`
[1] 3

$`1199_at`
[1] 1

$`1200_at`
[1] 1

$`1201_at`
[1] 1

$`1202_g_at`
[1] 1

$`1203_at`
[1] 1

$`1204_at`
[1] 1

$`1205_at`
[1] 1

$`1206_at`
[1] 1

$`1207_at`
[1] 2

$`1208_at`
[1] 1

$`1209_at`
[1] 1

$`120_at`
[1] 1

$`1210_s_at`
[1] 2

$`1211_s_at`
[1] 1

$`1212_at`
[1] 1

$`1213_at`
[1] 3

$`1214_s_at`
[1] 1

$`1217_g_at`
[1] 1

$`1218_at`
[1] 1

$`1219_at`
[1] 1

$`121_at`
[1] 1

$`1220_g_at`
[1] 1

$`1221_at`
[1] 2

$`1222_at`
[1] 1

$`1223_at`
[1] 1

$`1224_at`
[1] 3

$`1225_g_at`
[1] 3

$`1226_at`
[1] 1

$`1227_g_at`
[1] 1

$`1228_s_at`
[1] 3

$`1229_at`
[1] 2

$`122_at`
[1] 3

$`1230_g_at`
[1] 2

$`1231_at`
[1] 1

$`1232_s_at`
[1] 1

$`1233_s_at`
[1] 2

$`1234_at`
[1] 2

$`1235_at`
[1] 5

$`1236_s_at`
[1] 2

$`1237_at`
[1] 6

$`1238_at`
[1] 3

$`1239_s_at`
[1] 2

$`123_at`
[1] 1

$`1240_at`
[1] 2

$`1241_at`
[1] 2

$`1242_at`
[1] 3

$`1243_at`
[1] 1

$`1244_at`
[1] 1

$`1245_i_at`
[1] 1

$`1246_at`
[1] 1

$`1247_g_at`
[1] 1

$`1248_at`
[1] 2

$`1249_at`
[1] 1

$`1250_at`
[1] 1

$`1251_g_at`
[1] 2

$`1252_at`
[1] 1

$`1253_at`
[1] 1

$`1254_at`
[1] 1

$`1255_g_at`
[1] 1

$`1256_at`
[1] 2

$`1257_s_at`
[1] 1

$`1258_s_at`
[1] 1

$`1259_at`
[1] 2

$`1260_s_at`
[1] 1

$`1261_i_at`
[1] 1

$`1262_s_at`
[1] 1

$`1263_at`
[1] 1

$`1264_at`
[1] 3

$`1265_g_at`
[1] 3

$`1266_s_at`
[1] 2

$`1267_at`
[1] 1

$`1268_at`
[1] 2

$`1269_at`
[1] 4

$`126_s_at`
[1] 1

$`1270_at`
[1] 2

$`1271_g_at`
[1] 1

$`1272_at`
[1] 1

$`1273_r_at`
[1] 1

$`1274_s_at`
[1] 1

$`1275_at`
[1] 1

$`1276_g_at`
[1] 2

$`1277_at`
[1] 1

$`1278_at`
[1] 2

$`1279_s_at`
[1] 1

$`1280_i_at`
[1] 1

$`1281_f_at`
[1] 1

$`1282_s_at`
[1] 2

$`1283_at`
[1] 3

$`1284_at`
[1] 1

$`1285_at`
[1] 1

$`1286_s_at`
[1] 1

$`1287_at`
[1] 1

$`1288_s_at`
[1] 1

$`1289_at`
[1] 1

$`128_at`
[1] 1

$`1290_g_at`
[1] 1

$`1291_s_at`
[1] 2

$`1292_at`
[1] 1

$`1293_s_at`
[1] 1

$`1294_at`
[1] 1

$`1295_at`
[1] 1

$`1296_at`
[1] 1

$`1297_at`
[1] 2

$`1298_at`
[1] 4

$`1299_at`
[1] 1

$`129_g_at`
[1] 1

$`1300_at`
[1] 1

$`1303_at`
[1] 4

$`1304_at`
[1] 1

$`1305_s_at`
[1] 1

$`1306_at`
[1] 4

$`1307_at`
[1] 1

$`1308_g_at`
[1] 1

$`1309_at`
[1] 1

$`130_s_at`
[1] 2

$`1310_at`
[1] 3

$`1311_at`
[1] 1

$`1312_at`
[1] 1

$`1313_at`
[1] 1

$`1314_at`
[1] 1

$`1315_at`
[1] 1

$`1316_at`
[1] 3

$`1317_at`
[1] 1

$`1318_at`
[1] 2

$`1319_at`
[1] 1

$`131_at`
[1] 1

$`1320_at`
[1] 1

$`1321_s_at`
[1] 1

$`1322_at`
[1] 1

$`1323_at`
[1] 6

$`1324_at`
[1] 2

$`1325_at`
[1] 2

$`1326_at`
[1] 3

$`1327_s_at`
[1] 1

$`1328_at`
[1] 3

$`1329_s_at`
[1] 1

$`1330_at`
[1] 1

$`1331_s_at`
[1] 2

$`1332_f_at`
[1] 1

$`1333_f_at`
[1] 1

$`1334_s_at`
[1] 1

$`1335_at`
[1] 1

$`1336_s_at`
[1] 1

$`1337_s_at`
[1] 3

$`1338_s_at`
[1] 1

$`1339_s_at`
[1] 1

$`133_at`
[1] 2

$`1340_s_at`
[1] 3

$`1341_at`
[1] 1

$`1342_g_at`
[1] 1

$`1343_s_at`
[1] 1

$`1344_at`
[1] 3

$`1345_s_at`
[1] 3

$`1346_at`
[1] 1

$`1347_at`
[1] 3

$`1348_s_at`
[1] 1

$`1349_at`
[1] 1

$`134_at`
[1] 2

$`1350_at`
[1] 1

$`1351_at`
[1] 1

$`1352_at`
[1] 1

$`1353_g_at`
[1] 1

$`1354_at`
[1] 5

$`1355_g_at`
[1] 5

$`1356_at`
[1] 2

$`1357_at`
[1] 2

$`1358_s_at`
[1] 1

$`1359_at`
[1] 1

$`135_g_at`
[1] 2

$`1360_at`
[1] 1

$`1361_at`
[1] 1

$`1362_s_at`
[1] 12

$`1363_at`
[1] 6

$`1364_at`
[1] 1

$`1365_at`
[1] 1

$`1366_i_at`
[1] 1

$`1367_f_at`
[1] 1

$`1368_at`
[1] 2

$`1369_s_at`
[1] 1

$`136_at`
[1] 1

$`1370_at`
[1] 1

$`1371_s_at`
[1] 1

$`1372_at`
[1] 1

$`1373_at`
[1] 2

$`1374_g_at`
[1] 2

$`1375_s_at`
[1] 1

$`1376_at`
[1] 1

$`1377_at`
[1] 1

$`1378_g_at`
[1] 1

$`1379_at`
[1] 1

$`137_at`
[1] 1

$`1380_at`
[1] 1

$`1381_at`
[1] 4

$`1382_at`
[1] 1

$`1383_at`
[1] 2

$`1384_at`
[1] 5

$`1385_at`
[1] 1

$`1386_at`
[1] 1

$`1387_at`
[1] 1

$`1388_g_at`
[1] 1

$`1389_at`
[1] 4

$`138_at`
[1] 1

$`1390_s_at`
[1] 1

$`1391_s_at`
[1] 1

$`1392_at`
[1] 2

$`1393_at`
[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 4

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[1] 4

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 2

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[1] 3

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[1] 3

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 4

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[1] 2

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[1] 1

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[1] 1

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[1] 2

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[1] 2

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 4

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 3

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 2

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[1] 1

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[1] 2

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[1] 2

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[1] 1

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[1] 2

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[1] 3

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[1] 2

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 7

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 2

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[1] 2

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[1] 2

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 3

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 4

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 8

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[1] 2

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 4

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 14

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[1] 8

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 3

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 3

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 3

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 2

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 2

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[1] 2

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1] 1

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[1]